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This page was generated on 2021-10-15 15:06:44 -0400 (Fri, 15 Oct 2021).

CHECK results for myvariant on machv2

To the developers/maintainers of the myvariant package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/myvariant.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1240/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
myvariant 1.22.0  (landing page)
Adam Mark, Chunlei Wu
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/myvariant
git_branch: RELEASE_3_13
git_last_commit: 926053d
git_last_commit_date: 2021-05-19 12:15:12 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: myvariant
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:myvariant.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings myvariant_1.22.0.tar.gz
StartedAt: 2021-10-14 21:37:25 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 21:42:55 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 329.6 seconds
RetCode: 0
Status:   OK  
CheckDir: myvariant.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:myvariant.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings myvariant_1.22.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/myvariant.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘myvariant/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘myvariant’ version ‘1.22.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘myvariant’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.convertColumn4csv: no visible binding for global variable ‘is’
.df2DF: no visible binding for global variable ‘as’
.getIndels: no visible binding for global variable ‘REF’
.getIndels: no visible binding for global variable ‘ALT’
.unnest.df : <anonymous>: no visible global function definition for
  ‘is’
.unnest.df : <anonymous>: no visible global function definition for
  ‘setNames’
MyVariant: no visible global function definition for ‘new’
formatHgvs: no visible global function definition for
  ‘seqlevelsStyle<-’
validMyVariantObject: no visible global function definition for ‘slot’
.request.get,MyVariant: no visible global function definition for
  ‘capture.output’
.request.post,MyVariant: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  ALT REF as capture.output is new seqlevelsStyle<- setNames slot
Consider adding
  importFrom("methods", "as", "is", "new", "slot")
  importFrom("stats", "setNames")
  importFrom("utils", "capture.output")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/myvariant.Rcheck/00check.log’
for details.



Installation output

myvariant.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL myvariant
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘myvariant’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (myvariant)

Tests output


Example timings

myvariant.Rcheck/myvariant-Ex.timings

nameusersystemelapsed
MyVariant-class0.0020.0010.004
MyVariant0.0020.0010.003
formatHgvs2.2820.1032.389
formatSingleHgvs0.0010.0000.002
getVariant0.1900.0470.547
getVariants0.0810.0100.307
metadata0.0220.0100.145
queryVariant0.1030.0200.354
queryVariants0.0000.0000.001